User: Vitis

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Vitis2.2k
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8 years, 2 months ago
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A plant geneticist from a taxonomist and naturalist background. Now trying to bridge classic genetics and evolutionary biology with ever-expanding genomic data and bioinformatic tools.

Posts by Vitis

<prev • 316 results • page 1 of 32 • next >
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Comment: C: GATK JointDiscovery Error - Java Heap Space?
... Then I don't understand. Could you post this to GATK help forum? ...
written 1 day ago by Vitis2.2k
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Comment: C: GATK JointDiscovery Error - Java Heap Space?
... Did it give you the same "heap space" message and "RuntimeTotalMemory" after you specified 600G and ran the command? ...
written 1 day ago by Vitis2.2k
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Comment: C: GATK JointDiscovery Error - Java Heap Space?
... Probably does not need 600G, since it only used about 3G. I would start with specifying 32G~64G. ...
written 1 day ago by Vitis2.2k
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Comment: C: Question about generate a mappability mask file for non-human species
... Can you a make a reproducible case and report to SNPable regions or raise a possible issue? Without the exact same data and a reproducible example it will be hard to figure out what went wrong. ...
written 1 day ago by Vitis2.2k
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Answer: A: How to replicate vcftool's sliding window SNP density?
... Create a window file in BED format and use 'bedtools intersect' to intersect VCF and the window file. I believe there is an option to report number of overlaps, which in your case, would be number of SNPs in the windows. Please see: https://bedtools.readthedocs.io/en/latest/ ...
written 2 days ago by Vitis2.2k
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Answer: A: Efficiently run blat for long sequences
... Are you aligning spliced transcripts to genome assemblies, which requires opening big gaps (for introns)? If not, I'd suggest you to try minimap aligner: https://github.com/lh3/minimap2. There is an option to deal with substantially diverged sequences. If you're mapping spliced transcripts to genome ...
written 2 days ago by Vitis2.2k
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Comment: C: Question about generate a mappability mask file for non-human species
... Can you calculate length of FASTA entries before and after masking, for example, for chromosome 1? Based on the documentation, applying the mask only changes the low mappability regions into lower cases, and the sequence length should stay same. Can you confirm this in your data? ...
written 2 days ago by Vitis2.2k
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Answer: A: Shotgun metagenomics high duplication read rate - how high is too high?
... Sometimes high duplication rate is a result of excessive PCR enrichments of libraries before sequencing (Illumina platform). I would image metagenomic samples are pretty diverse so that it is less likely you've exhausted all kinds of unique molecules in the samples. I'd suggest you to take a look at ...
written 2 days ago by Vitis2.2k
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Comment: C: Read Count Differences in Amplicon Sequencing
... Any normalization of the individual libraries before sequencing? ...
written 9 weeks ago by Vitis2.2k
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Answer: A: ref and alt allele count from BAM file
... Both BAM and VCF can be used for this. In VCF, you would be looking for the values in the AD field for each sample. For BAM, you may want to consider using PySAM's pileup engine to query the position and reads stacked at that position. Just be careful with indels when using PySAM, you'll have to add ...
written 12 weeks ago by Vitis2.2k

Latest awards to Vitis

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 6 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 6 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 7 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Rna-Seq Tag Count
Scholar 8 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 10 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Scholar 11 months ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Great Question 2.6 years ago, created a question with more than 5,000 views. For Mapping Rates From Bwa
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to run SnpEff for Tomato 2.5 (S_lycopersicum_chromosomes.2.50) reference, gf
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Ka/Ks Ratio For Within A Gene - Very Confused !!
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: How To Convert Centimorgan To Base Pair
Good Answer 4.2 years ago, created an answer that was upvoted at least 5 times. For A: A Result From Mummer Alignment
Popular Question 4.2 years ago, created a question with more than 1,000 views. For Housekeeping Gene Identifications
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Mapping Rates From Bwa
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Autobiographer 5.4 years ago, has more than 80 characters in the information field of the user's profile.
Guru 5.4 years ago, received more than 100 upvotes.
Centurion 5.4 years ago, created 100 posts.
Supporter 5.4 years ago, voted at least 25 times.
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Looking For A Good Open Source Command-Line Sanger Sequence Pairwise Assembler
Appreciated 7.5 years ago, created a post with more than 5 votes. For A: Rna-Seq Data Variant Calling
Teacher 7.5 years ago, created an answer with at least 3 up-votes. For A: Rna-Seq Data Variant Calling

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